The first one should definitely not be used for gameplay. It's far too fast for gameplay, even if it is realistic. Although I guess that's obvious. (And by the way, I don't think it's sped up, as the seconds in the top left must be there for some purpose. This is unless they were trying to fool viewers.)

I would even go so far as to say the second is a bit quick too. Plus, I would assume that the numbers would have to be less than this or the computer might explode, especially if there are multiple swarms. Also, can you even zoom out enough to get this view. It would be closer up and so the microbes would flit across the screen even more.

I don't think those buffalo in that bullalo video move as fast as those microbes. I think that speed would be accecptable. It's not unmanageably fast, but it's not slow either. It can't be too fast to be uncomfortable to view. I think your version is just a bit too fast.

I'm not sure that microbes trampling microbes would be an effective method. They could, however, surround the microbe preventing an escape...which would probably require a complex signal agent.

Edit: Sorry, I misread something. I think the buffalos are a fine speed.